8,862 research outputs found
Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package
Dynamic time warping is a popular technique for comparing time series, providing both a distance measure that is insensitive to local compression and stretches and the warping which optimally deforms one of the two input series onto the other. A variety of algorithms and constraints have been discussed in the literature. The dtw package provides an unification of them; it allows R users to compute time series alignments mixing freely a variety of continuity constraints, restriction windows, endpoints, local distance definitions, and so on. The package also provides functions for visualizing alignments and constraints using several classic diagram types.
Uncertainty in phylogenetic tree estimates
Estimating phylogenetic trees is an important problem in evolutionary
biology, environmental policy and medicine. Although trees are estimated, their
uncertainties are discarded by mathematicians working in tree space. Here we
explicitly model the multivariate uncertainty of tree estimates. We consider
both the cases where uncertainty information arises extrinsically (through
covariate information) and intrinsically (through the tree estimates
themselves). The importance of accounting for tree uncertainty in tree space is
demonstrated in two case studies. In the first instance, differences between
gene trees are small relative to their uncertainties, while in the second, the
differences are relatively large. Our main goal is visualization of tree
uncertainty, and we demonstrate advantages of our method with respect to
reproducibility, speed and preservation of topological differences compared to
visualization based on multidimensional scaling. The proposal highlights that
phylogenetic trees are estimated in an extremely high-dimensional space,
resulting in uncertainty information that cannot be discarded. Most
importantly, it is a method that allows biologists to diagnose whether
differences between gene trees are biologically meaningful, or due to
uncertainty in estimation.Comment: Final version accepted to Journal of Computational and Graphical
Statistic
Tools for Search Tree Visualization: The APT Tool
The control part of the execution of a constraint logic program can be conceptually shown as a search-tree, where nodes correspond to calis, and whose branches represent conjunctions and disjunctions. This tree represents the search space traversed by the program, and has also a direct
relationship with the amount of work performed by the program. The nodes of the tree can be used to display information regarding the state and origin of instantiation of the variables involved in each cali. This depiction can also be used for the enumeration process. These are the features implemented in APT, a tool which runs constraint logic programs while depicting a (modified) search-tree, keeping at the same time information about the state of the variables at every moment in the execution. This information can be used to replay the execution at will, both forwards and backwards in time. These views can be abstracted when the size of the execution requires it. The search-tree view is used as a framework onto which constraint-level visualizations (such as those presented in the following chapter) can be attached
Cosmic cookery : making a stereoscopic 3D animated movie.
This paper describes our experience making a short stereoscopic movie visualizing the development of structure in
the universe during the 13.7 billion years from the Big Bang to the present day. Aimed at a general audience for
the Royal Society's 2005 Summer Science Exhibition, the movie illustrates how the latest cosmological theories
based on dark matter and dark energy are capable of producing structures as complex as spiral galaxies and
allows the viewer to directly compare observations from the real universe with theoretical results. 3D is an
inherent feature of the cosmology data sets and stereoscopic visualization provides a natural way to present the
images to the viewer, in addition to allowing researchers to visualize these vast, complex data sets.
The presentation of the movie used passive, linearly polarized projection onto a 2m wide screen but it was
also required to playback on a Sharp RD3D display and in anaglyph projection at venues without dedicated
stereoscopic display equipment. Additionally lenticular prints were made from key images in the movie. We
discuss the following technical challenges during the stereoscopic production process; 1) Controlling the depth
presentation, 2) Editing the stereoscopic sequences, 3) Generating compressed movies in display speci¯c formats.
We conclude that the generation of high quality stereoscopic movie content using desktop tools and equipment
is feasible. This does require careful quality control and manual intervention but we believe these overheads
are worthwhile when presenting inherently 3D data as the result is signi¯cantly increased impact and better
understanding of complex 3D scenes
The Application of the Montage Image Mosaic Engine To The Visualization Of Astronomical Images
The Montage Image Mosaic Engine was designed as a scalable toolkit, written
in C for performance and portability across *nix platforms, that assembles FITS
images into mosaics. The code is freely available and has been widely used in
the astronomy and IT communities for research, product generation and for
developing next-generation cyber-infrastructure. Recently, it has begun to
finding applicability in the field of visualization. This has come about
because the toolkit design allows easy integration into scalable systems that
process data for subsequent visualization in a browser or client. And it
includes a visualization tool suitable for automation and for integration into
Python: mViewer creates, with a single command, complex multi-color images
overlaid with coordinate displays, labels, and observation footprints, and
includes an adaptive image histogram equalization method that preserves the
structure of a stretched image over its dynamic range. The Montage toolkit
contains functionality originally developed to support the creation and
management of mosaics but which also offers value to visualization: a
background rectification algorithm that reveals the faint structure in an
image; and tools for creating cutout and down-sampled versions of large images.
Version 5 of Montage offers support for visualizing data written in HEALPix
sky-tessellation scheme, and functionality for processing and organizing images
to comply with the TOAST sky-tessellation scheme required for consumption by
the World Wide Telescope (WWT). Four online tutorials enable readers to
reproduce and extend all the visualizations presented in this paper.Comment: 16 pages, 9 figures; accepted for publication in the PASP Special
Focus Issue: Techniques and Methods for Astrophysical Data Visualizatio
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